Tag: Annotation

AAT 20110305 – Analysis & Annotation of Genomic Sequences

AAT 20110305

:: DESCRIPTION

AAT (analysis and annotation tool) includes two sets of programs, one set (DPS/NAP) for comparing the query sequence with a protein database, and the other (DDS/GAP2) for comparing the query with a cDNA database (Huang et al., 1997). Each set contains a fast database search program and a rigorous alignment program. The database search program quickly identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence. The alignment program also reports the coordinates of exons in the query sequence.

::DEVELOPER

Xiaoqiu Huang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AAT

:: MORE INFORMATION

Citation:

Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. (1997).
A tool for analyzing and annotating genomic sequences, Genomics 46, 37-45.

GenBank2Treedyn 21 – Extract Annotations from GenBank Files

GenBank2Treedyn 21

:: DESCRIPTION

GenBank2Treedyn etract annotations from GenBank files for:
More convenient alignments and phylogeny (replace def line of fasta file by GI number)
Extremely powerfull annotations of phylogenetic trees with TreeDyn.

::DEVELOPER

Virtual Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 GenBank2Treedyn

:: MORE INFORMATION

GO-SCAN 2.2 – Gene Ontology for Significant Collection of Annotations

GO-SCAN 2.2

:: DESCRIPTION

GO-SCAN is a bioinformatics tool that selects and presents relevant Gene Ontology (GO) annotations for a gene “hit” list from an Affymetrix microarray experiment.

GO-SCAN Online Version

::DEVELOPER

Mathematical and Statistical Computing Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JMP

:: DOWNLOAD

 GO-SCAN

:: MORE INFORMATION

BreakSeq 1.3 – Structural Variants Annotation and Identification pipeline

BreakSeq 1.3

:: DESCRIPTION

BreakSeq is a pipeline for annotation, classification and analysis of Structural Variants (SVs) at single nucleotide resolution

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BreakSeq

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2010 Jan;28(1):47-55. Epub 2009 Dec 27.
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB.

KOBAS 2.0 – Annotation and Identification of Enriched Pathways and Diseases

KOBAS 2.0

:: DESCRIPTION

KOBAS  (KEGG Orthology Based Annotation System) is a web server that annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases.

::DEVELOPER

KOBAS Team

:: REQUIREMENTS

:: DOWNLOAD

 KOBAS

:: MORE INFORMATION

Citation

Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C. and Wei, L. (2011)
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Nucleic Acids Res, 39, W316-322

CgiHunter 1.0 – Exhaustive CpG Island Annotation

CgiHunter 1.0

:: DESCRIPTION

CgiHunter is a software for the annotation of CpG islands in genomic sequence. DNA sequence are accepted in FASTA format. The generated annotations are exhaustive i.e. all CpG island that matches the given parameters will be identified. CpG islands are genome regions with an elevated Guanine + Cytosine content (GC content) and a higher CpG dinucleotide frequency than observed in the bulk genome. More than half of the human gene promoters colocalize with CpG islands and their methylation status has been shown to correlate with the expression level of the associated genes. As a consequence, CpG islands are assumed to be hotspots of epigenetic regulation.

CgiHunter Online Version

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Python

:: DOWNLOAD

 CgiHunter

:: MORE INFORMATION

 

TreeDyn 198.3 – Dynamic Graphics & Annotations for Phylogenetic Analyses

TreeDyn 198.3

:: DESCRIPTION

TreeDyn is a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.

::DEVELOPER

GEMI Bioinformatics F. Chevenet

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

TreeDyn

:: MORE INFORMATION

Citation:

Chevenet F., Brun C., Banuls A.L., Jacq B. and R. Christen
TreeDyn: towards dynamic graphics and annotations for analyses of trees
BMC Bioinformatics 2006, 7:439

goldMINER 2.0.27 – Use CDD to Automate Sequence Annotation

goldMINER 2.0.27

:: DESCRIPTION

goldMINER automates local and remote searches against pFAM and CDD (Conserved-Domain Database, which integrates pFAM, SMART and COG, etc.) databases searches to annotate sequences such as expressed sequence tags (ESTs). It is the first software package to use the power of CDD at NCBI to automate sequence annotation.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

goldMINER

:: MORE INFORMATION

N/A

SPICE 0.9 – Protein Sequences, Structures & Annotations Browser

SPICE 0.9

:: DESCRIPTION

SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

::DEVELOPER

Andreas Prlic, Thomas Down, Tim Hubbard.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

SPICE

:: MORE INFORMATION

Citation:

Adding some SPICE to DAS
Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41
Andreas Prlic, Thomas A. Down and Tim J. P. Hubbard

annot8r 1.1.1 – BLAST based GO-EC-KEGG Annotation

annot8r 1.1.1

:: DESCRIPTION

annot8r is a tool for the annotation of protein or nucleotide sequences from non model organisms with GO terms, EC numbers and KEGG pathways. The annotation is based on BLAST similarity searches against annotated subsets of EMBL UniProt from which sequences with non-informative entries have been removed. GO, EC and KEGG annotations are saved as flat files and in a relational postgreSQL database to allow for more sophisticated searches within the results.

::DEVELOPER

Ralf Schmid and Mark Blaxter

:: REQUIREMENTS

:: DOWNLOAD

annot8r

:: MORE INFORMATION